The S-palmitoylome and DHHC-PAT interactome of Drosophila melanogaster S2R+ cells indicate a high degree of conservation to mammalian palmitoylomes

Protein S-palmitoylation, the addition of a long-chain fatty acid to target proteins, is among the most frequent reversible protein modifications in Metazoa, affecting subcellular protein localization, trafficking and protein-protein interactions. S-palmitoylated proteins are abundant in the neuronal system and are associated with neuronal diseases and cancer. Despite the importance of this post-translational modification, it has not been thoroughly studied in the model organism Drosophila melanogaster. Here we present the palmitoylome of Drosophila S2R+ cells, comprising 198 proteins, an estimated 3.5% of expressed genes in these cells. Comparison of orthologs between mammals and Drosophila suggests that S-palmitoylated proteins are more conserved between these distant phyla than non-S-palmitoylated proteins. To identify putative client proteins and interaction partners of the DHHC family of protein acyl-transferases (PATs) we established DHHC-BioID, a proximity biotinylation-based method. In S2R+ cells, ectopic expression of the DHHC-PAT dHip14-BioID in combination with Snap24 or an interaction-deficient Snap24-mutant as a negative control, resulted in biotinylation of Snap24 but not the Snap24-mutant. DHHC-BioID in S2R+ cells using 10 different DHHC-PATs as bait identified 520 putative DHHC-PAT interaction partners of which 48 were S-palmitoylated and are therefore putative DHHC-PAT client proteins. Comparison of putative client protein/DHHC-PAT combinations indicates that CG8314, CG5196, CG5880 and Patsas have a preference for transmembrane proteins, while S-palmitoylated proteins with the Hip14-interaction motif are most enriched by DHHC-BioID variants of approximated and dHip14. Finally, we show that BioID is active in larval and adult Drosophila and that dHip14-BioID rescues dHip14 mutant flies, indicating that DHHC-BioID is non-toxic. In summary we provide the first systematic analysis of a Drosophila palmitoylome. We show that DHHC-BioID is sensitive and specific enough to identify DHHC-PAT client proteins and provide DHHC-PAT assignment for ca. 25% of the S2R+ cell palmitoylome, providing a valuable resource. In addition, we establish DHHC-BioID as a useful concept for the identification of tissue-specific DHHC-PAT interactomes in Drosophila.


Introduction
Protein S-acylation, the attachment of a fatty acid to a cysteine residue of a protein via a thioester bond, is one of the most abundant reversible post-translational modifications in Metazoa [1,2]. Because the fatty acid palmitate is most frequently involved [3][4][5], protein S-acylation is often referred to as S-palmitoylation (used here) or just palmitoylation.
Though the functional effects of S-palmitoylation on target proteins are often specific, some common functions of S-palmitoylation have been identified. For example, S-palmitoylation of soluble proteins results either in the reversible regulation of their subcellular localization and trafficking, or in their tight membrane association (reviewed in [6]). In the case of transmembrane proteins, S-palmitoylation can affect trafficking, localization to specific membrane domains, complex formation with other proteins, interplay with other post-translational modifications and initiation of conformational changes ( [7] and reviewed in [8]). Thus, the effects of S-palmitoylation on target proteins are very diverse; the biological functions of target proteins include iron uptake (transferrin receptor) [9], ER quality control/ER Ca 2+ homeostasis (calnexin) [10] and integrin signaling [11]. Several S-palmitoylated proteins are associated with diseases such as cancer and neurological diseases [1], suggesting that a better understanding of protein S-palmitoylation and its effects on target protein function is of interest to biomedical research.
Most protein S-palmitoylation reactions are catalyzed by the DHHC protein S-acyltransferase family (DHHC-PATs), while the reverse process (de-acylation) is performed by thioesterases. DHHC-PAT enzymes are characterized by four to six transmembrane domains and the name-giving DHHC (Asp-His-His-Cys) motif in an approximately 50-residue-long cysteine-rich domain (CRD) [12]. The Saccharomyces cerevisiae genome codes for seven DHHC-PATs, 15 are found in Caenorhabditis elegans, 24 in most mammals and 22 in Drosophila melanogaster [12][13][14]. De-acylation is carried out by four thioesterases in mammals (palmitoyl-protein thioesterase 1 and 2 (PPT1 and PPT2, respectively) and acyl-protein thioesterase 1 and 2 (APT1 and APT2) and by three thioesterases in Drosophila (Ppt1, Ppt2 and Apt1 [14]). While PPT1 and PPT2 act in lysosomes to remove acyl chains from client proteins during lysosomal degradation [15,16], APT1 and APT2 are responsible for the dynamic S-palmitoylation/de-palmitoylation cycle at the cytoplasmic membrane [17]. In both, mammals and insects, the different thioesterases have substrate specificity and cannot substitute each other [14,18,19].
Although mammals and insects have approximately the same number of DHHC-PATs, there are several DHHC-PATs lacking clear orthology between the two clades [14]. Nine Drosophila DHHC-PAT genes are exclusively expressed in the adult testis, and five of these have a genomic arrangement indicating recent duplication events [14]. Seven of the other 13 DHHC-PATs are most abundantly expressed in nervous tissue [14]. Hence, S-palmitoylation seems to play important roles in neurons and the male reproductive organ of Drosophila. In mammals, the highest fraction of S-palmitoylated proteins is found in neuronal tissues [1]. Neither DHHC-PATs expressed specifically in the testis, nor a testis palmitoylome has been reported in mammals. It is unclear whether this is due to a lack of research or an indication that S-palmitoylation does not play an important role in the mammalian testis.
Despite the many known S-palmitoylated proteins in mammals (>5000 proteins [1,2]), not much is known in invertebrate model organisms [20]. In Drosophila, protein S-palmitoylation has mostly been studied in the context of specific proteins. For example, it was reported that the expression of the Drosophila ortholog of the DHHC-PAT Huntingtin-interacting protein 14 (dHip14) is required in the nervous system for survival to adulthood and that it interacts with SNAP25 and cysteine string protein (CSP) [21,22]. dHip14 function is also required for S-palmitoylation and secretion of the short gastrulation (Sog) protein [23]. The DHHC-PAT approximated (app), which is most similar to human DHHC-PATs DHHC9/DHHC14/ DHHC18, was shown to have DHHC-PAT-dependent and independent functions. app binds to and localizes Dachs to the apical junctional region of imaginal discs and palmitoylates the large protocadherin Fat, resulting in repression of Fat function and promoting tissue growth [24,25]. Finally, RNAi-mediated knockdown of CG5196, an ER-localized DHHC-PAT similar to human DHHC6, results in more (and smaller) units of Golgi-ER exit sites as well as an increased cell size phenotype [26]. A more comprehensive catalogue of S-palmitoylated proteins in Drosophila and its systematic analysis is so far lacking, but would provide a valuable resource for the community. Furthermore, tools to identify client proteins of DHHC-PATs on the proteomic scale and in specific tissues are yet to be developed.
To this end, we herein provide a detailed study of the palmitoylome of S2R+ cells and use a novel, BioID-based approach to identify potential DHHC-PAT interaction partners and putative client proteins of DHHC-PATs (proteins that are palmitoylated by a given DHHC-PAT).
pMT-GW-BioID-HA-puro was generated by digesting pGWvectorBirA(R118G)-HA with StuI and PmeI to liberate the Gateway Cassette (Invitrogen) together with the BioID-HA fragment. pMT-puro was linearized by digestion with EcoRV and ligated with the pGWvecorBirA (R118G)-HA digestion products. Ligation products were transformed into ccdB-survival bacteria (Invitrogen). Clones harboring pMT-GW-BioID-HA-puro were identified by differential antibiotic selection and validated by sequencing.
pUASTattB-dHip14-BioID-HA was generated by Enhanced Gibson Assembly (New England BioLabs) of a dHip14 5´UTR PCR product, a dHip14-BioID-HA PCR product, a dHip14 3´UTR PCR product and linearized pUASTattB. The 5´UTR and the 3´UTR of dHip14 were PCR amplified from genomic DNA and dHip14-BioID-HA was PCR amplified from pMT-dHip14-BioID-HA-puro using primers specified in S1 Table. pMT-FLAG-dSnap24, pMT-FLAG-Snap25-PA and pMT-FLAG-dCSP were generated by cloning the respective coding regions from cDNA (total RNA from flies or S2R+ cells reverse transcribed with RevertAid First Strand cDNA Synthesis Kit (Thermo-Fisher) according to the manufacturer's protocol), using Xho-FLAG-flanked forward primers and NotI-flanked reverse primers, respectively (S1 Table), and then ligated in XhoI/NotI-digested pMT-puro.

Mutagenesis of dSnap24 and dSnap25
Site-directed mutagenesis was performed using pMT-FLAG-SNAP24 (SNAP24 P120A) and pMT-FLAG-SNAP25 (SNAP25 P125A) as templates for amplification with PfuPlus DNA polymerase (Roboklon) in combination with the respective primers (S1 Table). Primers for mutagenesis were generated with the help of the Agilent Quickchange design tool. Parental DNA was digested via incubation with DpnI (New England BioLabs) before transforming the amplification products into CaCl 2 competent DH5alpha. Mutant plasmids were validated by Sanger sequencing.
For transient transfection cells were seeded and after 18 h cells were transfected with plasmid DNA using X-tremeGENE HP DNA transfection reagent (Roche), according to the manufacturer's protocol (for 12-well plate format: 800 μL of 500 000 cells/mL; 500 ng plasmid, ratio of plasmid to reagent 1:8).
To select for stable transfected cells, cells were cultured in selective medium containing 1 μg/μL Puromycin (Invitrogen) from approximately 5 days after transfection, depending on cell density.
Protein expression via the metallothionine promoter was induced by supplementing the growth medium with 0.25 mM CuSO 4 (Sigma). For BioID experiments, medium was further supplemented with 50 μM biotin (Sigma), unless indicated otherwise.
Transfected cells were harvested as follows, unless specified otherwise. 24-72 h after induction of protein expression cells were washed with phosphate buffered saline (PBS), scraped in a small volume of PBS, pelleted (6,000 x g, 5 min, 4˚C), resuspended in ice-cold RIPA buffer (50 mM Tris-HCl, pH 7.4, 1% NP-40, 0.25% Na-deoxycholate, 150 mM NaCl; 1 mM EDTA with protease inhibitor cocktail) and sonicated for 5 min in an ice-cold sonication bath and centrifuged (10 000 x g, 5 min, 4˚C) to remove insoluble debris. The supernatant was used immediately or stored at -80˚C.

Fly maintenance and generation of transgenic flies
Flies were maintained on sucrose instant mashed potato food (13 g/L agar, 49 g/L sucrose, 36 g/L instant mashed potato powder (demeter bio quality), 17 g/L dry yeast, 7.95 mL/L 10% Nipagen and 2.16 mL/L propionic acid) under a 12 h / 12 h light/dark cycle at 25˚C unless stated otherwise. CO 2 delivered through a CO 2 -pad stage was used for anesthesia for fly sorting. Biotin supplementation of fly food was achieved by adding the appropriate amount of 164 mM biotin in DMSO to fly food cooled to approximately 45˚C, followed by thorough mixing.

BioID in flies
For BioID experiments, the respective parents were allowed to lay eggs on the indicated food source for 24-48 h at 25˚C. After further 48 h vials were transferred to 30˚C. To prepare samples for WB, larvae or adult animals, heads, thoraces or abdomen were homogenized in cold RIPA buffer (50-100 μL per L3 larvae or adult) using a glass homogenizer or for small sample volumes a plastic micro pestle.

Acyl-RAC assay
Isolation of S-palmitoylated proteins was performed as previously described [31]. Briefly, S2R + cells were washed in PBS, scraped, pelleted (2000 x g, 4˚C, 5 min) and resuspended in Buffer A (25 mM HEPES, 25 mM NaCl, 1 mM EDTA, protease inhibitor cocktail, pH 7.5). After sonication, cell debris was removed by centrifugation (800 x g, 4˚C, 10 min), membranes were enriched by centrifugation of the resulting supernatant at 16,200 x g for 50 min and 4˚C. The pelleted membranes were lysed in Buffer A containing 0.5% Triton X-100.
Equal amounts of protein (1 mg for mass spectrometry) were diluted 1:2 with blocking buffer (100 mM HEPES, pH 7.5, 1 mM EDTA, 2.5% SDS, 2.5% MMTS) at 40˚C for 2 h. Proteins were precipitated at -20˚C for 20 min after addition of three volumes of ice cold acetone. The pellet was washed with 70% acetone, air dried and resuspended in 300 μL binding buffer (100 mM HEPES, 1.0 mM EDTA, 1% SDS, pH 7.5) followed by the addition of 0.03 g Thiopropyl Sepharose 6B beads (GE Healthcare) (washed with binding buffer). Either 2 M NH 2 OH, pH 7.5 (+HA samples) or 2 M Tris-HCl, pH 7.5 (-HA samples) was added to a final concentration of 0.5 M and proteins were allowed to bind at room temperature overnight on a rotator. Beads were washed 5 times with binding buffer before 20 μL 4x reducing Laemmli buffer were added. Bound proteins were recovered by incubation at 95˚C for 10 min followed by SDS-PAGE.

Protein identification by mass spectrometry
Eluted material from the beads was separated by 1D SDS-PAGE (NuPage 125 gels, Invitrogen). Separated proteins were visualized by colloidal Coomassie blue staining. The proteins were reduced with 60 μL 40 mM dithiothreitol (DTT; Sigma-Aldrich, Taufkirchen, Germany) in 50 mM TEAB, pH 8.5 at 57˚C for 30 min and alkylated with 60 μL 50 mM iodoacetamide (IAA; Sigma-Aldrich, Taufkirchen, Germany) in 50 mM TEAB, pH 8.5 at 25˚C for 20 min in the dark. Gel pieces were dehydrated with 60 μL 100% ACN and washed with 60 μL 50 mM TEAB, pH 8.5. A total of 30 μL 8 ng/μL in 50 mM TEAB trypsin solution (sequencing grade, Thermo-Fisher, Rockford, USA) was added to the dry gel pieces and incubated for 6 h at 37˚C. The reaction was quenched by the addition of 20 μL 0.1% trifluoroacetic acid (TFA; Biosolve, Valkenswaard, Netherlands). The resulting peptides were extracted by two dehydration steps in 20 μL ACN for 20 min each followed by washing in 30 μL 50 mM TEAB, pH 8.5. The supernatant from each extraction step was collected and dried in a vacuum concentrator before LC-MS analysis. Samples were diluted in 15 μL 0.1% TFA, 99.9% water.
Nanoflow LC-MS 2 analysis was performed with an Ultimate 3000 liquid chromatography system directly coupled to an Orbitrap Elite mass spectrometer (both Thermo Fisher, Bremen, Germany). Samples were delivered to an in-house packed analytical column (inner diameter 75 μm x 20 cm; CS-Chromatographie Service GmbH, Langerwehe, Germany) filled with 1.9 μm ReprosilPur-AQ 120 C18 material (Dr. Maisch, Ammerbuch-Entringen, Germany). Solvent A was 0.1% formic acid (FA; ProteoChem, Denver, CO, USA) and 1% ACN (Biosolve) in H 2 O (Bisolve). Solvent B was composed of 0.1% FA (ProteoChem), 10% H 2 O (Biosolve) and 89.9% ACN (Biosolve). Samples were loaded onto the analytical column for 20 min with 3% solvent B at a flow rate of 550 nL/min. Peptide separation was carried out with a 100 min linear gradient (3-23% solvent B) and a 20 min linear gradient (23-38% solvent B) with a reduced flow rate of 300 nL/min. The mass spectrometer was operated in data-dependent acquisition mode, automatically switching between MS and MS 2 . MS spectra (m/z 400-1600) were acquired in the Orbitrap at 60 000 (m/z 400) resolution. Fragmentation in the HCD cell was performed for up to 15 precursors, and the MS 2 spectra were acquired.

Data quantification and statistics
The raw mass spectrometry data were processed with MaxQuant [33]. The resulting protein intensities were normalized by the median difference between each sample and the negative controls. The log fold-changes and the respective significance of the change were calculated using proDA version 0.1.0 [34]. Unlike alternative methods that rely on imputation to handle missing values, proDA provides a principled statistical test and is better able to control the false discovery rate. proDA calculates a dropout curve for each protein intensity and combines it with empirical Bayesian priors to determine if the observed pattern of observed and missing values and the corresponding mean difference could be simply due to chance.
Relative promiscuous biotinylation in myc-BioID experiments was estimated by integrating streptavidin signals in each lane normalized to the expression of BioID or BioID2. In co-overexpression experiments, relative biotinylation signals of FLAG-dSNAP24/25/25 � and CSP detected via Western blot were quantified as follows: biotinylation raw signals were normalized to the relative expression of the correspondent DHHC-PAT-BioID and expression of the FLAG-tagged protein. To calculate fold-changes of biotinylation the normalized biotinylation signal of the sample was divided by the normalized biotinylation of the negative control sample (only DHHC-BioID expression but no FLAG-tagged protein expression). Ratios were then normalized by the values calculated in S2R+ cells not expressing any of the DHHC-PAT-BioID. One-way ANOVA (GraphPad Prism Version 5.0 for Windows/Mac OS, GraphPad Software, San Diego, California, USA) was used for statistical analyses.

Bioinformatic data analysis
Protein identifiers, sequences, descriptions, and gene names were obtained from UniProt [35]. The DRSC Integrative Ortholog Prediction Tool (DIOPT) was used to determine mammalian orthologs for the Drosophila proteins by searching against human, mouse and rat proteomes and selecting only those orthologs with the highest confidence [36]. The SwissPalm database was used to determine the S-palmitoylation state of mammalian proteins [2,37]. Mammalian proteins reported as S-palmitoylated by at least one targeted study, or by two different experimental techniques were additionally classified as high confidence. S-palmitoylation was predicted using the program CSS-Palm 4.0 with high threshold [38]. Functional enrichment analyses of Gene Ontology (GO) terms were performed using Fisher's Exact test and False Discovery Rate (FDR) for multiple testing correction, through the PANTHER overrepresentation tool [39,40].

Drosophila S2R+ cells express at least 198 S-palmitoylated proteins
Extensive proteomic data exist on the S-palmitoylation status of mammalian cell lines and tissues [1,2], however, very little is known about the degree of protein S-palmitoylation in Drosophila. Here, we used acyl-resin assisted capture (acyl-RAC) [31] and LC-MS/MS to purify and identify potentially S-palmitoylated proteins from the membrane fraction of S2R+ cells.
To deal with missing data in negative controls, a result of affinity purification, we applied a novel method that uses the overall dropout probability for each intensity and empirical Bayesian priors to calculate a principled statistical test [34].
We initially identified 1188 different proteins by mass spectrometry (S1 Data), then filtered for those significantly enriched by acyl-RAC (proteins with a fold change (FC) equal to or above 2 and a false discover rate (FDR) below 0.1), removed proteins lacking cysteine residues, and excluded six proteins considered to be false positives, e.g. enzymes with thioester bonds known to not play a role in S-palmitoylation in the sense of the here investigated reversible protein lipidation. This resulted in 198 proteins that we considered S-palmitoylated, of which 51 were highly enriched by acyl-RAC (FC > = 20) and thus additionally labelled as high confidence (HC) S-palmitoylated proteins ( Fig 1A, S1 Data).
Next, we compared our S2R+ cell palmitoylome to that of Drosophila instar L2 larvae [20]. Of the 159 S-palmitoylated proteins in larvae, 61 overlapped with 30% of the 198 S-palmitoylated proteins in S2R+ cells. 21 larval S-palmitoylated proteins overlapped with 2% of the 990 proteins that were not significantly S-palmitoylated in S2R+ cells (Fig 1B). This comparison may indicate that only a very small fraction of proteins that are not significantly S-palmitoylated in S2R+ cells are likely to be S-palmitoylated in another tissue. However, the identification of more S-palmitoylated proteins in S2R+ cells (198 proteins) than in larvae (159 proteins) was unexpected. Whole larvae are more complex than S2R+ cells and would be expected to contain a more diverse palmitoylome than the cell line. The difference is most likely due to technical reasons; we used acyl-RAC, whereas Strassburger et al. used acyl/biotin exchange (ABE) [41] for enrichment and purification of S-palmitoylated proteins. As ABE requires many precipitation and resolubilization steps it is more prone to loss of proteins than acyl-RAC. Also the data analysis strategies were different; we used MaxQuant for protein identification and label-free quantification while MuDPIT [41] was used by Strassburger et al [20], which may further contribute to differences in peptide detection, protein identification and protein quantification. Additionally, a mix of different tissues, as in whole larval homogenates may result in the dilution of tissue-specific S-palmitoylated proteins below the limit of detection so that only palmitoylated proteins that are expressed in several tissues or at high enough levels in a single tissue can be detected. Finally, a recent study showed that acyl-RAC and ABI do seem to have biases for certain types of palmitoylated proteins, explaining the unexpectedly low overlap between palmitoylomes obtained from similar samples using either method [42].

Palmitoylated proteins are overrepresented in orthologs of Drosophila and mammals
We used multiple approaches to assess the degree of conservation in protein S-palmitoylation between Drosophila and mammals. While the fraction of genes encoding for S-palmitoylated proteins in mammals is approximately 10-14% [1], our initial estimation in Drosophila is clearly lower: if we consider that S2R+ cells express 5885 genes on average as reported previously [43], the 198 proteins we determined as being S-palmitoylated represent only 3.4%. However, because technical limitations in proteomics are greater than for transcriptomics, this is likely an underestimate. Also, S2R+ cells may not be the cell type with the most diverse palmitoylome; in Drosophila, neuronal tissue and testes may yield higher numbers of S-palmitoylated proteins as the expression of several DHHC-PATs is most abundant in these tissues [14].
To estimate the percentage of palmitoylated proteins on the whole-body level in Drosophila, we determined the ratio between Drosophila proteins with S-palmitoylated mammalian orthologs and all Drosophila orthologs of mammalian proteins (Fig 1C; S3 Table). This number, 17.1%, is clearly higher than 10-14% palmitoylated proteins in the full mammalian proteome. Acyl-RAC dataset subjected to different filtering to identify proteins that are unlikely to be palmitoylated ("non-palmitoylated", FDR > = 0.1 or FC < 2), palmitoylated proteins with "normal" confidence ("NC", FDR < 0.1 and FC < 20 and FC > = 2), palmitoylated proteins with "high" confidence ("HC", FDR <0.1 and FC > = 20). (B) Overlap of our acyl-RAC dataset, consisting of the S2R + palmitoylome proteins (normal and high confidence) and proteins not considered to be palmitoylated, with the larval palmitoylome from Strassburger et al 2019 [20]. (C) Barplots indicate the fraction (%) of proteins that have a mammalian ortholog (left), that have a mammalian ortholog that is palmitoylated (center) and that have a mammalian ortholog that is palmitoylated with "high" confidence (right) in each of the protein sets defined above. The palmitoylation status of the mammalian orthologs was obtained from the SwissPalm database. (D) Barplot that shows the fraction (%) of proteins predicted to be palmitoylated by CSS-Palm in each of the protein sets. That S-palmitoylated proteins are enriched within the group of Drosophila/mammalian orthologs indicates a higher degree of evolutionary conservation of S-palmitoylated proteins. This is expected, as S-palmitoylated proteins perform many essential cellular functions [44,45]. However, 17.1% could also be an overestimation, as not each palmitoylated protein in mammals needs to be palmitoylated in Drosophila. However, determining the overlap of palmitoylated proteins between mammalian and Drosophila will require a much more detailed Drosophila palmitoylome that covers the same tissues as the mammalian palmitoylomes.
We did similar ortholog searches for the proteins in the three subsets from our acyl-RAC experiment, as defined above (palmitoylated, palmitoylated with high confidence, and nonpalmitoylated). As expected, the percentage of proteins with S-palmitoylated mammalian orthologs is much higher within the S2R+ palmitoylome (56.5% and 62.7%, in the palmitoylome sets with normal and high confidence, respectively) than in the complete proteome, thus supporting the validity of our experiment to recover real palmitoylated proteins (Fig 1C). Interestingly, 62.6% of non-palmitoylated proteins from the acyl-RAC dataset were also found to have mammalian S-palmitoylated orthologs; this could be an indication that there are likely proteins that are less frequently palmitoylated in S2R+ cells than in other cell types and tissues.
Overall, we suggest that the proportion of S-palmitoylated proteins in Drosophila is similar to that in mammals (10-14%) as the current proportion estimate for Drosophila ranges from 3.5% between 17.1%.

Prediction of protein S-palmitoylation in Drosophila using CSS-Palm may yield a high false-positive rate
As S-palmitoylation prediction programs are trained on available data that are biased towards mammals and currently lack sites from insects, it is not clear how reliable they are in Drosophila. However, the high apparent conservation between Drosophila and mammalian S-palmitoylated proteins suggests that they might nevertheless be applicable to insects. We thus applied CSS-Palm [38] to three groups within the acyl-RAC dataset: non-palmitoylated, S-palmitoylated (NC) and S-palmitoylated (HC), and in the Drosophila reference proteome for comparison. Surprisingly, 49% of proteins in the Drosophila reference proteome have at least one predicted site (Fig 1D), which is more than 10 times higher than the percentage we extrapolated from our palmitoylome dataset (3.5%), and 3 times higher than when using mammalian orthologs as a reference (17.1%). Within the acyl-RAC dataset, 44.5% of the 990 non-palmitoylated proteins and about 75% (74.8% and 78.4% of the normal confidence and high confidence S-palmitoylated proteins, respectively) are predicted to be S-palmitoylated. Hence, CSS-Palm seems to be able to predict these proteins in Drosophila. However, because a very high number of proteins predicted have very low experimental support (low FC in acyl-RAC) compared to a low number of predicted S-palmitoylated proteins with good experimental support (high FC, S1 Fig), it can be assumed that the false-positive rate is very high, unless experimental methods fail to identify a very large fraction of S-palmitoylated proteins.

Palmitoylated proteins in S2R+ cells are enriched for subcellular membrane compartments involved in vesiclular transport
We performed a Gene Ontology (GO) term enrichment analysis to obtain a functional profile of the S2R+ cells palmitoylome (most significant terms in Fig 2, full list in S4 Table). In the cellular component category, "endomembrane system" and "intrinsic component of the membrane" were the most significantly overrepresented terms, which can be interpreted as a confirmation of the general methodology, as membrane fractions of S2R+ cells were used as input for acyl-RAC. However, other enriched terms that point to particular endomembrane system components such as the plasma membrane, Golgi apparatus, endoplasmic reticulum, cytoplasmic vesicles, or organelle membranes in general, are in agreement with the known common compartments of S-palmitoylated proteins (membrane compartments in general and the ER/Golgi to cytoplasmic membrane system but excluding the nuclear and mitochondrial membranes) [12], and with the recently reported function of protein sorting for export from the Golgi apparatus [7].
Regarding their function, enrichment in the biological process and molecular function ontologies revealed that the palmitoylome of S2R+ cells mostly comprises proteins with localization and transporter activities, such as proteins involved in vesicle-mediated transport (e.g. SNARE proteins Bet1, Sec20 or Snap24), or transporter proteins that directly enable the movement of ions and molecules across membranes (e.g. Indy, JhI-21 or Nh3). Additional enriched functions include cell communication and signaling, particularly represented by the presence of the heterotrimetric G-protein alpha subunits Galphai, Galphao, Galphas, Galphaq and cta (GO cellular component: heterotrimetic G-protein complex, and GO molecular functions: Gprotein beta/gamma-subunit complex binding). Cycles of S-palmitoylation and de-acylation have previously been shown to regulate G protein-coupled receptor (GPCR) signaling activation and deactivation in a mammalian cell line [46] in a manner akin to the S-palmitoylationdependent regulation of H-and N-Ras-subcellular localization and signaling [47]. The biological process "protein S-palmitoylation" and the molecular function "protein-cysteine S-palmitoylatransferase activity" were also enriched, owing to the fact that of the 22 Drosophila   Fig 2. Most significantly enriched GO terms in the Drosophila S2R+ cell palmitoylome proteins. Each bar represents the enrichment score (-log10(FDR p-value) of a GO term in the dataset and they are separated in three main categories: cellular component (black), biological process (dark grey) and molecular function (light grey). These terms were manually selected to be the most representative and avoiding redundancy. Full list can be found in S4 Table. https://doi.org/10.1371/journal.pone.0261543.g002 DHHC-PATs, nine were identified in the acyl-RAC dataset, of which seven were considered part of the S2R+ cell palmitoylome (Dnz1, GABPI, CG1407, CG5196, CG8314, CG34449/ dZDHHC8 and dHip14) (S1 Data).
In conclusion, our data yielded the expected GO-term enrichments of S-palmitoylated proteins: membranes, endosomal/Golgi localization and transport, and S-palmitoylation. The dynamic S-palmitoylation of GPCR signaling proteins described in mammals might also be important in insects. This is interesting, as the GPCR repertoire of invertebrates and vertebrates varies considerably, suggesting an origin of G-protein S-palmitoylation prior to the formation of the major GPCR superfamilies found in mammals [48].

DHHC-BioID is specific enough to identify DHHC-PAT substrates
With the palmitoylome of S2R+ cells at hand, our next aim was to establish a method to identify potential substrates of DHHC-PATs. We used our S2R+ cell line as a starting point and explored the use of DHHC-PAT-BioID in combination with UAS/GAL4-dependent cell-specific expression in the fruit fly [49] as a means to acquire cell-specific DHHC-PAT interactomes. After optimizing BioID in S2R+ cells, larvae and adult flies (S1 Appendix), we proceeded to test whether DHHC-PAT-BioID constituted a feasible method to identify client proteins of DHHC-PATs. To this end we chose the well-characterized Drosophila DHHC-PAT Huntingtin-interacting protein 14 (dHip14). dHip14 is the ortholog of the mammalian HIP14 protein with which it shares the client proteins cysteine string protein (CSP) and Snap25 [21,22]. In addition, HIP14 is the only known DHHC-PAT for which a conserved recognition motif in its client proteins has been identified (-[VIAP]-[VIT]-X-X-Q-P-) and which recognition is mediated by ANK repeats in the N-terminal cytoplasmic arm of HIP14 [50]. Importantly, the mutation of a proline to an alanine residue prevents the interaction of client proteins with HIP14 and thereby their S-palmitoylation [50].
To study the specificity of DHHC-BioID, we co-overexpressed dHip14-BioID or two unrelated DHHC-PATs, CG5620-BioID and CG6618-BioID, with N-terminally FLAG-tag-fused wt Snap25 (FLAG-Snap25) or the proline mutant (FLAG-Snap25 � ). Using Western blot and streptavidin probes to detect protein biotinylation we found a considerable increase in biotinylation of a protein with the relative molecular mass of dSnap25 in cells expressing dHip14-BioID and FLAG-dSnap25, but not in cells expressing dHip14-BioID and FLAG-dSnap25 � or in cells expressing any of the other two DHHC-PAT-BioID fusion proteins in combination with FLAG-dSnap25 (Fig 3A-3C for quantified data). Increased biotinylation was taken as evidence of successful DHHC-PAT-BioID expression and activity, while anti-FLAG antibodies were used to identify FLAG-tagged proteins and to confirm comparable expression levels of FLAG-Snap25 and FLAG-Snap25 � .
To further explore the specificity of the system, we extended the analysis to 10 selected DHHC-PATs localized in various organelles, excluding the remaining 12 DHHC-PATs which show highly testis-or ovary-specific expression patterns [14,52]. Thus, DHHC-BioID constructs were generated for, CG6017 (dHip14), CG8314, CG5196, CG5880, CG6618 (Patsas), CG5620 (app), CG17257 (GABPI), CG1407, CG4676 and CG6627 (Dnz1) and co-overexpressed either with FLAG-dSnap24 (a ubiquitously expressed SNAP25-homolog, FlyBase.org and [53]) or FLAG-dSnap25 (Fig 3D and 3F and S3 Fig). Expression of the DHHC-PAT-BioID fusion proteins alone served as the respective negative control to judge the pattern of protein biotinylation of each DHHC-PAT-BioID construct when the FLAG-tagged client proteins were not co-overexpressed (Fig 3D and 3E). dSnap24 has not been described as a dHip14-BioID substrate, but it shares a high degree of sequence similarity with dSnap25, including the Hip14-interaction motif (Fig 3A). Quantification of signals at the respective molecular masses of dSnap24 and dSnap25 revealed that three DHHC-PATs resulted in consistently increased biotinylation (CG1407, Hip14 and Dnz1) (Fig 3D and 3F). We also observed a reproducible interaction of the non-enzymatic DHHC-PAT GABPI with dSnap24. As CG1407, Dnz1 and GABPI lack the ANK repeat domain that is necessary for the interaction of a DHHC-PAT with the Hip14 interaction motif, the biotinyation of these proteins is likely independent of this motif. To test this, we chose Dnz1-BioID as its putative interaction with dSnap24 and dSnap25 seemed the most robust. As expected, co-expression of Dnz1-BioID with either, dSnap25, or the Hip14 interaction motif mutant dSnap25 � , resulted in a biotinylation signal of either protein´s apparent molecular weight (S2 Fig). From these results we conclude that DHHC-PAT-BioID is specific enough to recognize the interaction of dHip14 and dSnap25 even in overexpression conditions, which usually have the tendency of enhancing non-specific interactions. Putative interactions of CG1407, Dnz1 and GABPI with dSnap24/dSnap25 could be due to real interactions or just very close proximity of these proteins during e.g. vesicular transport.

dHip14-BioID is sensitive enough to detect endogenous dSnap24 and dCSP
Finally, we wanted to know whether DHHC-PAT-BioID was sensitive enough to detect endogenous levels of DHHC-PAT interaction partners. To do this, we expressed dHip14-BioID in S2R+ cells, then affinity purified the biotinylated proteins with streptavidin beads and identified these proteins by mass spectrometry. S2R+ cells exposed to the same treatment but not expressing DHHC-BioID were used as a negative control. We found dSnap24 and dCSP among the proteins recovered from dHip14-BioID expressing S2R+ cells (S2 Data). dSnap24 was robustly identified in all three dHip14-BioID samples and absent in two out of three control samples, while dCSP was only detected in one of three dHip14-BioID samples. The lower recovery of dCSP was in agreement with our co-overexpression experiments, in which biotinylation of dCSP co-overexpressed with dHip14-BioID was also markedly weaker than biotinylation of dSnap24 or dSnap25, even if expressed at similar levels (S2 Fig). Nevertheless, in this initial dHip14-BioID proteomic dataset (S2 Data), we also found several proteins (e.g. Golgin-245, Golgin-84, Sec24AB, Sec24CD and Ergic-53) associated with the Golgi apparatus location of dHip14 [14] and vesicle transport. Whether or not they are valid client proteins or interaction partners cannot be judged at this point, as other DHHC-BioID datasets would be required to estimate specificity.
Taken together, the recovery of the endogenous dHip14 client proteins, dSnap24 and dCSP shows that DHHC-PAT-BioID is sensitive enough to detect endogenous interaction partners of DHHC-PATs.

Dnz1 does not rescue Hip14 mutant flies
As we retrieved Dnz1 as a novel interaction partner of dSnap24 and dSnap25 (by western blot ;  Fig 3, S3 Fig) and dSnap24 and dCSP (by proteomics; S2 and S3 Data), we asked whether this interaction could rescue lethality of Hip14 mutants. In dHip14 mutant flies failure of dCSP-Spalmitoylation and hence membrane association has been identified as the cause of lethality; expression of dCSP fused to the transmembrane domain of neuronal synaptobrevin rescues pharate adult lethality of dHip14-mutant flies [22]. We thus reasoned that if Dnz1 interacts with and palmitoylates dCSP in a dHip14-independent manner, overexpression of Dnz1 in neurons should rescue pharate lethality of dHip14 mutant flies. To test this, we crossed mutant dHip14 flies carrying UAS-Dnz1 or UAS-dHip14-BioID (w -; If/CyO; UAS-Dnz1-3xHA, dHi-p14 ex12 /TM6B, Tb, Hu or respectively w -; UAS-dHip14-BioID/CyO; dHip14 2 /TM6B, Tb, Hu) with mutant dHip14 flies carrying the elavGAL4 driver for neuronal expression (w -; elavGAL4/ CyO; Hip14 2 /TM6B, Tb, Hu). Flies cultured at 25˚C were rescued by neuronal expression of dHip14-BioID but not by neuronal expression of Dnz1 (Table 1). These results show that even though Dnz1 and dHip14 both interact with Snap24, dHip14 is required for S-palmitoylation of dCSP. As Dnz1 and dHip14 reside in different subcellular compartments (endoplasmic reticulum and Golgi apparatus, respectively [14]), it is likely that they do not have complementary functions. However, the exact function of Dnz1, in the context of its interaction with dCSP, is not clear. At this stage, our results only allow us to draw the conclusion that Dnz1 on its own is not able to palmitoylate dCSP in fly neuronal tissue.

DHHC-PAT-BioID identifies 180 putative DHHC-PAT interaction partners in S2R+ cells
With the proof of principle showing that DHHC-PAT-BioID is specific and sensitive enough to identify endogenous interaction partners of DHHC-PATs, we wanted to investigate the interactomes and putative client spectra of the aforementioned 10 DHHC-PATs in S2R+ cells. Thus, we carried out two independent experiments, each experiment consisting of three biological replicates per DHHC-PAT-BioID. In total, we identified 2162 proteins of which 487 proteins were enriched in at least one DHHC-PAT-BioID sample (FDR<0.1, FC> = 2) compared with the negative control (S2R+ cells transfected with empty vector) (S3 Data). These were subdivided in 193 proteins that reproducibly interacted with at least one common DHHC-PATs in both experiments (high-confidence DHHC-PAT interactors) and 294 nonreproducible putative interactors (low-confidence DHHC-PAT interactors) (Fig 4A). When compared to our previously established palmitoylome, we found that 25% of the palmitoylated proteins in S2R+ cells could be assigned to at least one DHHC-PAT; this suggests that DHHC-BioID is missing the interactions of three-quarters of palmitoylated proteins with their DHHC-PATs. Probable reasons could be: (1) only 10 out of the 13 non-testis-specific DHHC-PAT genes in Drosophila were investigated here; (2) of each of these, only one splice variant was used, whereas several genes are known to produce two or more differentially spliced products (S4 Fig); (3) DHHC-PAT interactions with their client proteins are transient and biotinylation efficiency of BioID used under the conditions described here may be limited to recovery of endogenous proteins that are abundant or undergo several cycles of S-palmitoylation/de-palmitoylation, increasing their chances to be labeled with a biotin.
Our main aim was to explore the potential of using proximity biotinylation for the identification of DHHC-PAT interactors. We find that this technique is suitable for the analysis of individual substrate candidates when ectopically expressing DHHC-BioID. This method may eventually permit the conclusive identification of specific DHHC-PAT interactions in Drosophila adult or larval tissues.

DHHC-PAT-BioID interactors: S-palmitoylated substrates or neighboring proteins?
Since DHHC-PAT-BioID will not only recover client proteins that are S-palmitoylated by the DHHC-PAT under investigation, but also any other neighboring, accessory or co-localized   [32], a significant challenge is to distinguish real client proteins of the DHHC-PAT from other interaction partners or neighbors that are not functionally relevant. Analyses of yeast and mammalian DHHC-PAT/client proteins have shown that most client proteins are unlikely to be S-palmitoylated by more than 4-6 different DHHC-PATs [54,55]. In addition, in yeast, most of the seven DHHC-PATs can be knocked out without adverse effects, indicating that there is a large degree of redundancy between different DHHC-PATs [54]. To test whether the average number of DHHC-PATs that can palmitoylate the same protein could be derived from our dataset we checked whether the fraction of palmitoylated proteins that interact with a given number of DHHC-PATs peaked a specific number of DHHC-PATs. However, no such effect could be observed and no endogenous threshold could be derived from the dataset itself (S5 Fig). However, filtering for proteins that have a certain maximum number of DHHC-PAT-interactions will allow the identification of DHHC-PATs that actually have different substrate spectra. Of course, there might be protein/DHHC-PAT interactions that do occur with all DHHC-PATs, e.g. accessory proteins/enzymes, trafficking proteins, etc. So, to give a more complete picture, we present results from both approaches, i.e. a dataset to which no threshold for the number of DHHC-PAT interactions was applied, and a dataset in which a maximum of six DHHC-PATinteractions (the maximum number of different DHHC-PATs known to palmitoylate the same protein in mammals [54,55]) was allowed (Fig 4B-4G).
Little is currently known about different DHHC-PAT substrate specificities. According to two studies mammalian and yeast DHHC-PATs can be grouped according to their preference for soluble proteins and for integral membrane proteins [56,57]. On the other hand, a highthroughput study in yeast reported that substrates of DHHC-PATs are possibly better grouped by the relative position of the cysteine residue that is S-palmitoylated (N-terminal, C-terminal or in respect to transmembrane domains) [54]. In our DHHC-PAT-interactome we found a certain bias of CG8314, CG5196, CG5880 and Patsas towards proteins with transmembrane domains (TMD); almost 40% of all of their interactors (both S-palmitoylated and non-S-palmitoylated proteins) had at least one TMD and around 80% of their S-palmitoylated interactors were TMD proteins (Fig 4D and 4E). For most other DHHC-PATs, the fraction of Spalmitoylated transmembrane substrates was around 50-60%, with the exception of CG6618 (approximated), which was markedly lower (30%).
To further investigate substrate specificities of DHHC-PATs, we checked for each DHHC-PAT in our study the fraction of proteins with the Hip14 interaction motif [50]. It ranged from 7% to 20% in different DHHC-PATs (Fig 4F). Furthermore, we observed an interesting correlation when considering S-palmitoylated substrates exclusively. Those DHHC-PATs that had the highest fraction of transmembrane proteins among their S-palmitoylated substrates also had the lowest fraction of S-palmitoylated substrates with the Hip14 interaction motif (0% in most cases) and vice versa, with the DHHC-PATs approximated and Hip14 showing the highest ratios (Fig 4E and 4G). This broad subdivision of DHHC-PATs into two groups according to their substrate preferences was confirmed by clustering analyses (S6 Fig). These results and our co-expression experiments with Snap24, Snap25 and dCSP (Fig 3) show that even though Patsas and Hip14 both contain ANK repeats in their N-terminal cytoplasmic domains, only Hip14 interacts with its substrates via the Hip14 interaction motif. This is also in agreement with the observation that the two proteins are more distantly related than their mammalian counterparts (DHHC13/HIP14-like and ZDHHC17/HIP14) [14]. Conversely, we confirmed in the case of Dnz1, a DHHC-PAT that showed an interaction with Snap24/Snap25 in our DHHC-BioID assay but lacks ANK repeats, that this interaction is not via the Hip14-interaction motif (S2 Fig). In addition, we also found that GABPI is among the DHHC-PATs with a broader range of interactors (Fig 4B), which may be indicating a role as a substrate-presenter rather than a palmitoyl-transferase [51].

Conclusions
With our work we markedly increased the number of experimentally identified palmitoylated proteins in Drosophila and give a first detailed comparison between Drosophila and mammalian palmitoylomes, as well as highlight certain conserved functions, such as GPCR/G-protein signaling, where both groups are apparently similar in palmitoylation despite substantial differences elsewhere.
We also established DHHC-BioID as a novel method to identify proteins interacting with DHHC-PATs. This approach shows promise to also work in a tissue specific manner in Drosophila, and when combined with palmitoylome data increases the chance to identify real client proteins for DHHC-PATs on the proteomic level.  Table. Complete GO enrichment analysis results of the D. melanogaster S2R+ cell palmitoylome proteins. Overrepresented GO terms associated to the 198 S-palmitoylated proteins were determined with Fisher's exact tests, using the whole D. melanogaster's proteome as reference. FDR correction was applied to Fisher's test P-values to adjust for multiple testing. GO terms were considered significantly enriched if FDR adjusted P-value < 0.05. GO terms are separated in the three main ontologies (cellular component, biological process and molecular function) and sorted by their FDR adjusted P-value. Excel file containing the combined total of 2162 proteins and columns detailing the analyzed results (p-value, FDR adjusted p-value, fold change, and the number of samples (sample count) where a peptide for a given DHHC-PAT-BioID/protein interaction was identified by mass-spec) for each of the 10 DHHC-PAT, in each of the two experiments. Each of the two experiments was comprised of three (in some cases five) samples (three consecutively, not in parallel, repeated cell-culture experiments). Additional columns, summarize the number and identity of those interactions we estimated to be significant, as well as the palmitoylation status of the proteins according to our Acyl-RAC results, the larvae palmitoylome, mammalian ortholog palmitoylation and predicted palmitoylation.